5OFN

Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster.

Holzer, S.Yan, J.Kilkenny, M.L.Bell, S.D.Pellegrini, L.

(2017) Nat Commun 8: 1718-1718

  • DOI: https://doi.org/10.1038/s41467-017-01707-w
  • Primary Citation of Related Structures:  
    5OF3, 5OFN

  • PubMed Abstract: 

    DNA replication depends on primase, the specialised polymerase responsible for synthesis of the RNA primers that are elongated by the replicative DNA polymerases. In eukaryotic and archaeal replication, primase is a heterodimer of two subunits, PriS and PriL. Recently, a third primase subunit named PriX was identified in the archaeon Sulfolobus solfataricus. PriX is essential for primer synthesis and is structurally related to the Fe-S cluster domain of eukaryotic PriL. Here we show that PriX contains a nucleotide-binding site required for primer synthesis, and demonstrate equivalence of nucleotide-binding residues in PriX with eukaryotic PriL residues that are known to be important for primer synthesis. A primase chimera, where PriX is fused to a truncated version of PriL lacking the Fe-S cluster domain retains wild-type levels of primer synthesis. Our evidence shows that PriX has replaced PriL as the subunit that endows primase with the unique ability to initiate nucleic acid synthesis. Importantly, our findings reveal that the Fe-S cluster is not required for primer synthesis.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit PriS330Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: priSpriASSO1048
EC: 2.7.7
UniProt
Find proteins for Q97Z83 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97Z83 
Go to UniProtKB:  Q97Z83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97Z83
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit PriL,PriL-X fusion protein
B, C
324Saccharolobus solfataricus P2Saccharolobus solfataricus
This entity is chimeric
Mutation(s): 0 
Gene Names: priLpriBSSO0557C21_042
UniProt
Find proteins for Q9UWW1 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UWW1 
Go to UniProtKB:  Q9UWW1
Find proteins for Q97ZS7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97ZS7 
Go to UniProtKB:  Q97ZS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ97ZS7Q9UWW1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.052α = 90
b = 36.348β = 96.91
c = 110.941γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description